Well, it looks like you got a lot of advice. All I can add is raising kids in this environment is tough. Right now your wife might be a liberal witness but if she longs to have the family that goes to the hall together she may change. That happened to me and I can tell you that it was not pretty.
As a former cultist, myself, I can relate. I used to also be subjected to the black and white thinking that comes from the more fundamentalist type churches and I use to dream of having the 'perfect Christian family.' I no longer qualify for that now as my beliefs have changed dramatically and don't fit in with the traditional Christian mold anymore. I guess, like you, I am more agnostic now.
Your wife may go back and forth between wanting to be balanced and wanting to drag he kids to every meeting because it is best for their 'spiritual health.' For me, it is sad to watch my wife not trust her own thinking when it comes to her battle between what she really wants to do and what she is 'supposed' to do. I try to give my kids a variety of experiences, teach about a variety of beliefs, and challenge dogmatic thinking (like Super Why being magical and wrong). As a former fundy cultist I am all too familiar with this type of idiotic thinking.